-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpredict_seqs.sh
75 lines (62 loc) · 2.28 KB
/
predict_seqs.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
#!/bin/bash
export CUDA_VISIBLE_DEVICES=0
s1_predict=./data/input/s1_seq_to_seq.csv
s1_modelfile=./model/seqs_s1
s1_result=./data/output/s1_results.csv
s2_predict=./data/input/s2_seq_to_seq.csv
s2_modelfile=./model/seqs_s2
s2_result=./data/output/s2_results.csv
s_co_result=./data/output/s_co_results.csv
# s_predict=./data/input/s_seq_to_seq.csv
# s_modelfile=./model/seqs_s
# s_vallina_result=./data/output/s_vallina_results.csv
python ./flax/summarization/predict_summarization_flax.py \
--output_dir ./seqs_s1_predict \
--model_name_or_path ${s1_modelfile}\
--tokenizer_name ${s1_modelfile} \
--test_file=${s1_predict} \
--validation_file=${s1_predict} \
--baseline_fname=./transformers/examples/flax/summarization/spike_reference.fa \
--protein=s1 \
--generate_file_name=${s1_result} \
--do_predict --predict_with_generate\
--overwrite_output_dir \
--per_device_eval_batch_size 64 \
--max_source_length 1400 \
--max_target_length 695 > ./predict_s1_seqs.log 2>&1
wait
python ./flax/summarization/predict_summarization_flax.py \
--output_dir ./seqs_s2_predict \
--model_name_or_path ${s2_modelfile} \
--tokenizer_name ${s2_modelfile} \
--test_file=${s2_predict} \
--validation_file=${s2_predict} \
--baseline_fname=./transformers/examples/flax/summarization/spike_reference.fa \
--protein=s2 \
--generate_file_name=${s2_result} \
--do_predict --predict_with_generate\
--overwrite_output_dir \
--per_device_eval_batch_size 64 \
--max_source_length 1200 \
--max_target_length 590 > ./predcit_s2_seqs.log 2>&1
wait
python ./data/output/postprocess_data.py \
--s1-filename=${s1_result} \
--s2-filename=${s2_result} \
--s-results-filename=${s_co_result} > ./merge.log 2>&1
# python ./flax/summarization/predict_summarization_flax.py \
# --output_dir ./seqs_s_predict \
# --model_name_or_path ${s_modelfile} \
# --tokenizer_name ${s_modelfile} \
# --test_file=${s_predict} \
# --validation_file=${s_predict} \
# --protein=s \
# --baseline_fname=./transformers/examples/flax/summarization/spike_reference.fa \
# --do_predict --predict_with_generate\
# --generate_file_name ${s_vallina_result} \
# --overwrite_output_dir \
# --grammer False \
# --csc False \
# --per_device_eval_batch_size 64 \
# --max_source_length 1300 \
# --max_target_length 1300 > ./predict_s_seqs.log 2>&1